It is not about the marketing. Inside the App Store, pricing options are severly limited. This is problematic - especially for "pro" apps. The fact that there is no update pricing makes it hard for many professional app developers.
It is so problematic that there are so many pro apps in the App Store that are even the top selling ones. Or in other words: the reality is the exact opposite from your fear. Not having trial and upgrade options is and has been a problem since day 1 for every kind of application in the App Store. It is not limited to games, pro apps, etc.
With the iOS store, you can only keep making money and finance the development of your app if your user base is growing as in new users buying the app. This may be fine for many games and fun apps, but in the professional segment you have a very stable "niche" user base. With this, you will stop making money at some point and get into trouble
This is the exact problem I was talking about. Developers thinking that they the App Store is going to do the selling. Biiiiiig mistake. If you are going to sell via the App Store you are a business (hence why you need to fill out certain forms, need to have an American VAT number, etc.) and just like any other business you have to actively try to make money. Not only do you have to get the word out about your existence, you also have to keep on doing this and offer much more than just 1 app unless you like going bankrupt. If you want to have recurring revenue than selling a product is most definitely the wrong approach because it will only provide revenue 1 time. What you need is a subscription because that means revenue every month. The problem with that: not many buyers are open for that kind of model.
The latter is something you'll see with nearly every business software. There are quite a lot of licensing models where you pay for the applications itself and where you have to pay extra in order to use the mobile apps. The mobile apps are usually free.
Also, niche products are usually not a big issue since there is a certain audience who is far more likely to buy it. We see it with a lot of different products, especially the luxury ones. That's why you often see these businesses either asking a lot of money for the product, going the extra mile and/or offering cheaper products (usually under a different brand and usually aimed at the general public and not the niche audience). That's how they are able to survive. However, not all of them have to do this. A lot of them can survive just fine with only selling their niche product.
I think people are forgetting the basics of running a company just as much as they are forgetting that the App Store is first and foremost a means of distributing ones software. It is not meant as a way for running ones business (read: you don't just create an app, put it in the app store and then profit, there is more involved).
The financial problems of the App Store are entirely Apple's doing. The fact the Mac App Store has failed to attract any serious heavyweights and is regularly losing some of its star products, just shows how hostile the App Store policies are to developers.
There is one very important thing you and many others keep forgetting: OS X is an existing ecosystem, very well established and with a lot of expectations. Unlike iOS it isn't build with an app store in mind nor is it tightly integrated (read: the only way to install apps). It is very complex to create an app store for OS X. The way it is now doesn't work all that well but I seriously doubt that the way it is done in Ubuntu and the like will work (there will be issues with liability and testing because they'll run into the same issues as any company will). Maybe will have to draw the conclusion that an app store for OS X simply doesn't work.
Btw, none of what you mentioned is financial. They are all technical or due to an existing ecosystem.
the problem is I want to use Apple iWork programs but they are so lacking compared to Office.
I really want numbers to be able to hyperlink to locally stored PDF's and a built in solution to Pages to manage and edit PDF's signing and stamping etc.
As far as I know you can't do that with MS Office either. You can only use their own format and it is quite limited compared to their desktop parts.